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991.
We present a parametric family of regression models for interval-censored event-time (survival) data that accomodates both fixed (e.g. baseline) and time-dependent covariates. The model employs a three-parameter family of survival distributions that includes the Weibull, negative binomial, and log-logistic distributions as special cases, and can be applied to data with left, right, interval, or non-censored event times. Standard methods, such as Newton-Raphson, can be employed to estimate the model and the resulting estimates have an asymptotically normal distribution about the true values with a covariance matrix that is consistently estimated by the information function. The deviance function is described to assess model fit and a robust sandwich estimate of the covariance may also be employed to provide asymptotically robust inferences when the model assumptions do not apply. Spline functions may also be employed to allow for non-linear covariates. The model is applied to data from a long-term study of type 1 diabetes to describe the effects of longitudinal measures of glycemia (HbA1c) over time (the time-dependent covariate) on the risk of progression of diabetic retinopathy (eye disease), an interval-censored event-time outcome. 相似文献
992.
Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics 总被引:2,自引:0,他引:2
993.
Michael Hackenberg Christopher Previti Pedro Luis Luque-Escamilla Pedro Carpena José Martínez-Aroza José L Oliver 《BMC bioinformatics》2006,7(1):446-13
Background
Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content. 相似文献994.
Ekaterina Y Steshina Michael S Carr Elena A Glick Aleksey Yevtodiyenko Oliver K Appelbe Jennifer V Schmidt 《BMC genetics》2006,7(1):1-21
Background
The Dlk1 and Gtl2 genes define a region of mouse chromosome 12 that is subject to genomic imprinting, the parental allele-specific expression of a gene. Although imprinted genes play important roles in growth and development, the mechanisms by which imprinting is established and maintained are poorly understood. Differentially methylated regions (DMRs), which carry methylation on only one parental allele, are involved in imprinting control at many loci. The Dlk1-Gtl2 region contains three known DMRs, the Dlk1 DMR in the 3' region of Dlk1, the intergenic DMR 15 kb upstream of Gtl2, and the Gtl2 DMR at the Gtl2 promoter. Three mouse models are analyzed here that provide new information about the regulation of Dlk1-Gtl2 imprinting.Results
A previously existing insertional mutation (Gtl2lacZ), and a targeted deletion in which the Gtl2 upstream region was replaced by a Neo cassette (Gtl2Δ5'Neo), display partial lethality and dwarfism upon paternal inheritance. Molecular characterization shows that both mutations cause loss of imprinting and changes in expression of the Dlk1, Gtl2 and Meg8/Rian genes. Dlk1 levels are decreased upon paternal inheritance of either mutation, suggesting Dlk1 may be causative for the lethality and dwarfism. Loss of imprinting on the paternal chromosome in both Gtl2lacZ and Gtl2Δ5'Neo mice is accompanied by the loss of paternal-specific Gtl2 DMR methylation, while maternal loss of imprinting suggests a previously unknown regulatory role for the maternal Gtl2 DMR. Unexpectedly, when the Neo gene is excised, Gtl2Δ5' animals are of normal size, imprinting is unchanged and the Gtl2 DMR is properly methylated. The exogenous DNA sequences integrated upstream of Gtl2 are therefore responsible for the growth and imprinting effects.Conclusion
These data provide further evidence for the coregulation of the imprinted Dlk1 and Gtl2 genes, and support a role for Dlk1 as an important neonatal growth factor. The ability of the Gtl2lacZ and Gtl2Δ5'Neo mutations to cause long-range changes in imprinting and gene expression suggest that regional imprinting regulatory elements may lie in proximity to the integration site. 相似文献995.
Background
Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs, RibAlign has been developed to fill this gap. 相似文献996.
Oliver Laule Matthias Hirsch-Hoffmann Tomas Hruz Wilhelm Gruissem Philip Zimmermann 《BMC bioinformatics》2006,7(1):311-8
Background
Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from prior knowledge or experimentation. Knowledge obtained from meta-analyzing compendia of expression data with annotation libraries can provide significant clues in understanding gene and network function, resulting in better hypotheses that can be tested in the laboratory. 相似文献997.
The quartz crystal microbalance with dissipation monitoring (QCM-D) was used to monitor the deposition of adhesive extracellular polymeric substances (EPS) employed by the marine biofouling diatoms Craspedostauros australis Cox and Amphora coffeaeformis Cleve during initial adhesion and subsequent motility. Upon injection into the QCM chamber, initial negative frequency (f) shifts and positive dissipation (D) shifts were measured that correlated to cells impacting and adhering to the QCM sensor surface. Following this "initial adhesion" response, f continued to decrease while D increased logarithmically. Rather than the result of any cell morphological alterations at the substrate surface, the shifts were correlated to the time-dependent deposition of EPS upon the substrate surface as a result of cellular motility, or gliding. Experiments utilizing comparable cell concentrations of the diatom species C. australis and A. coffeaeformis revealed significant differences between the parameter responses recorded, where A. coffeaeformis produced Deltaf and DeltaD values of -32 Hz and 6.6, and C. australis produced values of -82 Hz and 42, respectively, after 20 h post-inoculation. The viscoelastic properties of the adhered EPS adlayer from both species were examined via a Deltaf/DeltaD plot, providing reproducible signature "ratio" values for each species that likely correlate to differences in EPS interactions with the substrate that may be associated directly to differences in the fouling potential of the two species. There is a distinct lack of knowledge regarding the chemical nature of the adhesive polymers engaged, and few quantitative techniques are applicable to the study of diatom EPS. We propose that QCM-D may be a useful tool in identifying differences in the EPS employed by diatoms of different fouling potential. 相似文献
998.
Perica's J Oliver P Guitard R Pico C Palou A 《The Journal of nutritional biochemistry》2001,12(8):444-449
The influence of age and gender on uncoupling protein 2 (UCP2) expression and its relationship with leptin expression in subcutaneous adipose tissue has been studied in humans. Samples of subcutaneous adipose tissue were obtained from 41 adult subjects (20 women and 21 men), with an age range of 28 to 84 years, and body mass index (BMI) of 19 to 36 Kgm(minus sign2). UCP2 and leptin mRNA expression was determined by northern blot. In women, both leptin and UCP2 expression in the subcutaneous adipose tissue increased significantly with age (r = 0.490 p < 0.05 and r = 0.475 p < 0.05, respectively). In men, in contrast, a negative correlation was found between leptin expression and age (r = minus sign0.678 p < 0.001), while no significant correlation was apparent between UCP2 expression and age (r = minus sign0.077). In addition, there was a positive correlation between UCP2 and leptin expression in women (r = 0.656 p < 0.01). These data show important gender dependent differences in the age-related changes in leptin and UCP2 expression in subcutaneous adipose tissue in humans. 相似文献
999.
1000.
M Hoppert M Valdez M Enseleit W Theilmann O Valerius GH Braus C Föst W Liebl 《Systematic and applied microbiology》2012,35(5):279-290
Several closely related strains of the thermophilic bacterium Dictyoglomus have been isolated from various hot springs on the Philippine archipelago. These strains as well as Dictyoglomus thermophilum H-6-12 were analyzed in view of the structure-functional relationships of the cell envelopes. All envelopes of Dictyoglomus strains show several peculiar features that are apparently either unique for the genus or common for other phylogenetically related Thermotogales. The filamentous cells develop pili at the cell poles, guided by large columnar protein assemblies that traverse the periplasm. Filamentous protein complexes span the periplasmic space at the longitudinal sides of the cell. By the end of the exponential growth phase, Dictyoglomus strains form multicellular aggregates ("rotund bodies") inside a compartment surrounded by a single, continuous outer envelope. The formation of these rotund bodies which are also found in some other deeply branching thermophilic phyla (Thermotoga, Thermus) was studied in detail. The transition between unicellular and multicellular lifestyle can be explained by the partial detachment of a protoplast from the outer envelope during cell division. When the outer envelope is partially detached from the protoplast, mechanical forces generated by protoplast elongation may drive cell rearrangement of daughter cells inside the compartment. During the following rounds of cell division, the overall shape of the compartment changes from spindle-like to globular geometry. Analysis of subcellular fractions of Dictyoglomus cells shows that glucan hydrolases are associated with the compartment. This feature is discussed in view of the multicellular life style of Dictyoglomus. 相似文献